3VZB Transferase Inhibitor date Oct 10, 2012
title Crystal Structure Of Sphingosine Kinase 1
authors X.Min, N.P.Walker, Z.Wang
compound source
Molecule: Sphingosine Kinase 1
Chain: A, B, C
Fragment: Unp Residues 9-364
Synonym: Sk 1, Spk 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Sf9
Gene: Sphk1, Sphk, Spk
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Htb
symmetry Space Group: C 2 2 21
R_factor 0.213 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
101.859 226.263 106.487 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EDO, SO4, SQS enzyme Transferase E.C. BRENDA
A, C, B
  • lipid kinase activity
  • sphinganine kinase activity
  • sphingosine-1-phosphate rece...

  • Primary referenceMolecular Basis of Sphingosine Kinase 1 Substrate Recognition and Catalysis., Wang Z, Min X, Xiao SH, Johnstone S, Romanow W, Meininger D, Xu H, Liu J, Dai J, An S, Thibault S, Walker N, Structure. 2013 Apr 16. pii: S0969-2126(13)00086-5. doi:, 10.1016/j.str.2013.02.025. PMID:23602659
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (3vzb.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3vzb.pdb2.gz) 60 Kb
  • Biological Unit Coordinates (3vzb.pdb3.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3VZB
  • CSU: Contacts of Structural Units for 3VZB
  • Structure Factors (1216 Kb)
  • Retrieve 3VZB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VZB from S2C, [Save to disk]
  • Re-refined 3vzb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VZB in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3VZB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3VZB, from MSDmotif at EBI
  • Fold representative 3vzb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vzb_A] [3vzb_B] [3vzb_C] [3vzb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VZB: [DAGKc ] by SMART
  • Other resources with information on 3VZB
  • Community annotation for 3VZB at PDBWiki (http://pdbwiki.org)

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